New subject: recon-all ERROR, no idea why

23 Jun 2014

This is dying somewhere in the MNI nu_correct code. Look at the
orig.mgz
to see if that looks ok

On 06/23/2014 03:58 PM, Remy Wahnoun wrote:
>
> Thanks Douglas,
>
> I definitely appreciate your help.
>
> Here is what it Spit out,
>
> *Rémy Wahnoun, PhD*
>
> Biomedical Research Group Manager
>
> Barrow Neurological Institute at Phoenix Children's Hospital
>
> Adjunct Faculty, Arizona State University
>
> /www.NeuralControl.net <http://www.NeuralControl.net>
<http://www.neuralcontrol.net/>/
>
> set echo = 1 ;
>
> set debug = 1 ;
>
> set debug = 1
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 11 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --n
>
> shift
>
> switch ( $flag )
>
> switch ( --n )
>
> if ( $#argv == 0 ) goto arg1err ;
>
> if ( 10 == 0 ) goto arg1err
>
> set nIters = $argv[1] ; shift ;
>
> set nIters = 1
>
> shift
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 9 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --proto-iters
>
> shift
>
> switch ( $flag )
>
> switch ( --proto-iters )
>
> if ( $#argv == 0 ) goto arg1err ;
>
> if ( 8 == 0 ) goto arg1err
>
> set nProtoIters = $argv[1] ; shift ;
>
> set nProtoIters = 1000
>
> shift
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 7 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --distance
>
> shift
>
> switch ( $flag )
>
> switch ( --distance )
>
> if ( $#argv == 0 ) goto arg1err ;
>
> if ( 6 == 0 ) goto arg1err
>
> set Distance = $argv[1] ; shift ;
>
> set Distance = 50
>
> shift
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 5 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --no-rescale
>
> shift
>
> switch ( $flag )
>
> switch ( --no-rescale )
>
> set DoRescale = 0 ;
>
> set DoRescale = 0
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 4 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --i
>
> shift
>
> switch ( $flag )
>
> switch ( --i )
>
> if ( $#argv == 0 ) goto arg1err ;
>
> if ( 3 == 0 ) goto arg1err
>
> set InVol = $argv[1] ; shift ;
>
> set InVol = orig.mgz
>
> shift
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 2 != 0 )
>
> set flag = $argv[1] ; shift ;
>
> set flag = --o
>
> shift
>
> switch ( $flag )
>
> switch ( --o )
>
> if ( $#argv == 0 ) goto arg1err ;
>
> if ( 1 == 0 ) goto arg1err
>
> set OutVol = $argv[1] ; shift ;
>
> set OutVol = orig_nu.mgz
>
> shift
>
> breaksw
>
> breaksw
>
> end
>
> end
>
> while ( $#argv != 0 )
>
> while ( 0 != 0 )
>
> goto parse_args_return ;
>
> goto parse_args_return
>
> goto check_params ;
>
> goto check_params
>
> if ( $#InVol == 0 ) then
>
> if ( 1 == 0 ) then
>
> if ( ! -e $InVol ) then
>
> if ( ! -e orig.mgz ) then
>
> if ( $#OutVol == 0 ) then
>
> if ( 1 == 0 ) then
>
> goto check_params_return ;
>
> goto check_params_return
>
> set OutDir = `dirname $OutVol` ;
>
> set OutDir = `dirname $OutVol`
>
> dirname orig_nu.mgz
>
> mkdir -p $OutDir ;
>
> mkdir -p .
>
> if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log
>
> if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log
>
> set LF = ./mri_nu_correct.mni.log
>
> if ( -e $LF ) mv $LF $LF.bak
>
> if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log
> ./mri_nu_correct.mni.log.bak
>
> mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak
>
> pwd | tee -a $LF
>
> pwd
>
> tee -a ./mri_nu_correct.mni.log
>
> /media/sf_Imagery/FreeSurfer/xx/mri
>
> which mri_nu_correct.mni | tee -a $LF
>
> which mri_nu_correct.mni
>
> tee -a ./mri_nu_correct.mni.log
>
> /usr/local/freesurfer/bin/mri_nu_correct.mni
>
> echo $cmdargs | tee -a $LF
>
> echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
> orig.mgz --o orig_nu.mgz
>
> tee -a ./mri_nu_correct.mni.log
>
> --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
> orig.mgz --o orig_nu.mgz
>
> echo "nIters $nIters" | tee -a $LF
>
> echo nIters 1
>
> tee -a ./mri_nu_correct.mni.log
>
> nIters 1
>
> echo $VERSION | tee -a $LF
>
> tee -a ./mri_nu_correct.mni.log
>
> echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42
nicks Exp $
>
> $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
>
> uname -a | tee -a $LF
>
> uname -a
>
> tee -a ./mri_nu_correct.mni.log
>
> Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4
> 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux
>
> date | tee -a $LF
>
> date
>
> tee -a ./mri_nu_correct.mni.log
>
> Mon Jun 23 15:32:45 EDT 2014
>
> nu_correct -version | tee -a $LF
>
> nu_correct -version
>
> tee -a ./mri_nu_correct.mni.log
>
> Program nu_correct, built from:
>
> Package MNI N3, version 1.10, compiled by nicks@fishie
> (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13
>
> if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$
>
> if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745
>
> set tmpdir = ./tmp.mri_nu_correct.mni.1745
>
> mkdir -p $tmpdir
>
> mkdir -p ./tmp.mri_nu_correct.mni.1745
>
> echo "tmpdir is $tmpdir" | tee -a $LF
>
> echo tmpdir is ./tmp.mri_nu_correct.mni.1745
>
> tee -a ./mri_nu_correct.mni.log
>
> tmpdir is ./tmp.mri_nu_correct.mni.1745
>
> set cmd = ( mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc )
>
> set cmd = ( mri_convert orig.mgz
./tmp.mri_nu_correct.mni.1745/nu0.mnc )
>
> if ( $UseFloat ) set cmd = ( $cmd -odt float )
>
> if ( 1 ) set cmd = ( mri_convert orig.mgz
> ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float )
>
> set cmd = ( mri_convert orig.mgz
./tmp.mri_nu_correct.mni.1745/nu0.mnc
> -odt float )
>
> pwd | & tee -a $LF
>
> pwd
>
> tee -a ./mri_nu_correct.mni.log
>
> /media/sf_Imagery/FreeSurfer/xx/mri
>
> echo $cmd | & tee -a $LF
>
> echo mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc
-odt float
>
> tee -a ./mri_nu_correct.mni.log
>
> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt
float
>
> $cmd | & tee -a $LF
>
> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt
float
>
> tee -a ./mri_nu_correct.mni.log
>
> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt
float
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>
> reading from orig.mgz...
>
> TR=25.00, TE=5.36, TI=0.00, flip angle=30.00
>
> i_ras = (-1, 1.49012e-08, 0)
>
> j_ras = (0, 0, -1)
>
> k_ras = (-1.30385e-08, 1, -5.96046e-08)
>
> changing data type from uchar to float (noscale = 0)...
>
> writing to ./tmp.mri_nu_correct.mni.1745/nu0.mnc...
>
> if ( $status ) then
>
> if ( 0 ) then
>
> @ nthIter = 1 ;
>
> @ nthIter = 1
>
> while ( $nthIter < = $nIters )
>
> while ( 1 < = 1 )
>
> echo " " | & tee -a $LF
>
> echo
>
> tee -a ./mri_nu_correct.mni.log
>
> echo "--------------------------------------------------------" | &
> tee -a $LF
>
> echo --------------------------------------------------------
>
> tee -a ./mri_nu_correct.mni.log
>
> --------------------------------------------------------
>
> echo "Iteration $nthIter `date`" | & tee -a $LF
>
> echo Iteration 1 `date`
>
> tee -a ./mri_nu_correct.mni.log
>
> date
>
> Iteration 1 Mon Jun 23 15:32:49 EDT 2014
>
> @ m = $nthIter - 1
>
> @ m = 1 - 1
>
> set cmd = ( nu_correct -clobber $tmpdir/nu${m}.mnc
> $tmpdir/nu${nthIter}.mnc )
>
> set cmd = ( nu_correct -clobber
./tmp.mri_nu_correct.mni.1745/nu0.mnc
> ./tmp.mri_nu_correct.mni.1745/nu1.mnc )
>
> set cmd = ( $cmd -tmpdir ${tmpdir}/${m}/ ) ;
>
> set cmd = ( nu_correct -clobber
./tmp.mri_nu_correct.mni.1745/nu0.mnc
> ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir
> ./tmp.mri_nu_correct.mni.1745/0/ )
>
> if ( $#nProtoIters ) set cmd = ( $cmd -iterations $nProtoIters ) ;
>
> if ( 1 ) set cmd = ( nu_correct -clobber
> ./tmp.mri_nu_correct.mni.1745/nu0.mnc
> ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir
> ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 )
>
> set cmd = ( nu_correct -clobber
./tmp.mri_nu_correct.mni.1745/nu0.mnc
> ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir
> ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 )
>
> if ( $#StopThresh ) set cmd = ( $cmd -stop $StopThresh ) ;
>
> if ( 0 ) set cmd = ( nu_correct -clobber
> ./tmp.mri_nu_correct.mni.1745/nu0.mnc
> ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir
> ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -stop )
>
> if ( $#Distance ) set cmd = ( $cmd -distance $Distance ) ;
>
> if ( 1 ) set cmd = ( nu_correct -clobber
> ./tmp.mri_nu_correct.mni.1745/nu0.mnc
> ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir
> ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 )
>
> set cmd = ( nu_correct -clobber
./tmp.mri_nu_correct.mni.1745/nu0.mnc
> ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir
> ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 )
>
> if ( $#FWHM ) set cmd = ( $cmd -fwhm $FWHM ) ;
>
> if ( 0 ) set cmd = ( nu_correct -clobber
> ./tmp.mri_nu_correct.mni.1745/nu0.mnc
> ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir
> ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
-fwhm )
>
> echo $cmd | & tee -a $LF
>
> echo nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc
> ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir
> ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
>
> tee -a ./mri_nu_correct.mni.log
>
> nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc
> ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir
> ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
>
> $cmd | & tee -a $LF
>
> nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc
> ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir
> ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
>
> tee -a ./mri_nu_correct.mni.log
>
> [fsuser@xubuntu-VirtualBox:/media/sf_Imagery/FreeSurfer/xx/mri/]
> [2014-06-23 15:32:49] running:
>
> /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log
> -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask
> -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber
-nokeeptmp
> -tmpdir ./tmp.mri_nu_correct.mni.1745/0/
> ./tmp.mri_nu_correct.mni.1745/nu0.mnc
> ./tmp.mri_nu_correct.mni.1745/nu1.imp
>
> Assertion failed at line 827 in file templates/CachedArray.cc
>
> nu_estimate_np_and_em: crashed while running volume_stats
(termination
> status=256)
>
> nu_correct: crashed while running nu_estimate_np_and_em (termination
> status=256)
>
> if ( $status ) then
>
> if ( 0 ) then
>
> rm -f $tmpdir/nu${m}.mnc $tmpdir/nu${m}.imp
>
> rm -f ./tmp.mri_nu_correct.mni.1745/nu0.mnc
> ./tmp.mri_nu_correct.mni.1745/nu0.imp
>
> @ nthIter = $nthIter + 1 ;
>
> @ nthIter = 1 + 1
>
> echo " " | & tee -a $LF
>
> echo
>
> tee -a ./mri_nu_correct.mni.log
>
> end
>
> end
>
> while ( $nthIter < = $nIters )
>
> while ( 2 < = 1 )
>
> echo " " | & tee -a $LF
>
> echo
>
> tee -a ./mri_nu_correct.mni.log
>
> echo " " | & tee -a $LF
>
> echo
>
> tee -a ./mri_nu_correct.mni.log
>
> set numnc = $tmpdir/nu$nIters.mnc
>
> set numnc = ./tmp.mri_nu_correct.mni.1745/nu1.mnc
>
> if ( $DoRescale ) then
>
> if ( 0 ) then
>
> if ( ! -e $numnc ) then
>
> if ( ! -e ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) then
>
> echo "ERROR: file $numnc does not exist!" | & tee -a $LF
>
> echo ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not
exist!
>
> tee -a ./mri_nu_correct.mni.log
>
> ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist!
>
> exit 1 ;
>
> exit 1
>
>
------------------------------------------------------------------------
>
> This transmission, including any attachments, is for the sole use of
> the intended recipient (s) and may contain information that is
> confidential, proprietary, legally privileged, or otherwise
protected
> by law from disclosure. Any unauthorized review, use, copying,
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intended
> recipient, or the person responsible for delivering this to an
> addressee, you should notify the sender immediately by telephone
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> reply e-mail, and destroy all copies of the original message.
>
>
>
> _______________________________________________
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] recon-all ERROR, no idea why